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ChIPQC (version 1.6.1)
Quality metrics for ChIPseq data
Description
Quality metrics for ChIPseq data
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Link to current version
Version
Version
1.8.2
1.6.1
1.4.4
1.2.2
Version
1.6.1
License
GPL (>= 3)
Maintainer
Tom Carroll
Last Published
February 15th, 2017
Functions in ChIPQC (1.6.1)
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ChIPQC-data
Example data sets for
ChIPQC
package, each containing a
ChIPQCexperiment
object, as well as a pre-compiled blacklist for hg19.
ChIPQC-package
ChIPQC - Quality metrics for ChIPseq data
ChIPQC
Construct a
ChIPQCexperiment
object
frip-methods
Retrieve fraction of reads in peaks
mapped-methods
Retrieve numbers of mapped reads
fragmentlength-methods
Retrieve the estimated fragment length
averagepeaksignal-methods
Retrieve average peak profiles
ReadLengthFragmentLengthCrossCoverage-methods
Retrieve the cross coverage values when extending reads to the optimal fragment length.
QCannotation-methods
Retrieve an annotation description, or a processed annotation
ChIPQCsample-class
Class
"ChIPQCsample"
plotRap-methods
Generate reads in peaks plot
plotPrincomp-methods
Generate Principal Components Analysis plot for ChIP samples
QCmetrics-methods
Retrieve consolidated set of QC metrics
QCsample-methods
Retrieve sample objects associated with an experiment
QCcontrol-methods
Retrieve control objects associated with a sample
readlength-methods
Retrieve read length values
ReadLengthReadLengthCrossCoverage-methods
Retrieve the cross coverage values without extending reads
rip-methods
Retrieve numbers of reads overlapping peaks
ssd-methods
Retrieve SSD (squared sum of deviations) values of peak coverage
coveragehistogram-methods
Retrieve histogram data representing densities of coverage pileups
duplicates-methods
Retrieve numbers of duplicate reads.
flagtagcounts-methods
Retrieve numbers of reads that pass various filters
QCdba-methods
Retrieve the
DBA
object associated with an experiment
crosscoverage-methods
Retrieve the cross coverage values for a range of shift sizes
QCmetadata-methods
Retrieve metadata associated with an experiment
duplicateRate-methods
Retrieve duplication rates
plotRegi-methods
Generate relative enrichment of genomic features plot
plotSSD-methods
Generate SSD plot
ribl-methods
Retrieve numbers of reads overlapping blacklisted regions
RelativeCrossCoverage-methods
Retrieve the relative cross coverage values for a range of shift sizes
ChIPQCexperiment-class
ChIPQCexperiment instances
ChIPQCreport-methods
Generate a summary QC report
Normalisedaveragepeaksignal-methods
Retrieve normalised average peak profiles
peaks-methods
Retrieve peaks
plotFrip-methods
Generate fraction of reads in peaks plot
plotPeakProfile-methods
Generate peak profile plots
plotCC-methods
Generate Cross-Coverage plots
plotCorHeatmap-methods
Generate Correlation Heatmap for ChIP samples
plotCoverageHist-methods
Generate coverage histogram plot
plotFribl-methods
Generate fraction of reads in blacklist plot
reads-methods
Retrieve numbers of reads
regi-methods
Retrieve genomic profile information